gapless_msa: Remove Gaps in a MSA
In orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants
gapless_msa R Documentation
Remove Gaps in a MSA
Description
Removes gaps in a given msa.
Usage
gapless_msa(msa, seqtype = 'AA', df = TRUE, sfile = FALSE)
Arguments
msa
input alignment.
seqtype
the nature of the sequences: 'DNA' or 'AA'.
df
logical. When TRUE msa should be a matrix, when FALSE msa should be a string giving the path to a fasta file containing the alignment.
sfile
if different to FALSE, then it should be a string indicating the path to save a fasta alignment file.
Details
It should be noted that this function does not carry out the alignment itself.
Value
an alignment without gaps in form of matrix or a file containing such an alignment in fasta format.
See Also
msa
Examples
## Not run: gapless_msa(msa(sequences = c("APGW", "AGWC", "CWGA"),ids = c("a", "b", "c"))$ali)
orthGS documentation built on June 8, 2025, 12:37 p.m.
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| gapless_msa | R Documentation |
Remove Gaps in a MSA
Description
Removes gaps in a given msa.
Usage
gapless_msa(msa, seqtype = 'AA', df = TRUE, sfile = FALSE)
Arguments
msa |
input alignment. |
seqtype |
the nature of the sequences: 'DNA' or 'AA'. |
df |
logical. When TRUE msa should be a matrix, when FALSE msa should be a string giving the path to a fasta file containing the alignment. |
sfile |
if different to FALSE, then it should be a string indicating the path to save a fasta alignment file. |
Details
It should be noted that this function does not carry out the alignment itself.
Value
an alignment without gaps in form of matrix or a file containing such an alignment in fasta format.
See Also
msa
Examples
## Not run: gapless_msa(msa(sequences = c("APGW", "AGWC", "CWGA"),ids = c("a", "b", "c"))$ali)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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